Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 76 of 226
Found at i:28101180 original size:148 final size:146
Alignment explanation
Indices: 28100954--28101229 Score: 367
Period size: 148 Copynumber: 1.9 Consensus size: 146
28100944 AGTCTATTCT
* * ** * **
28100954 ACTGCAACTTCAGTGAGATAAGACTTGTAATTTCAATAAAGTCTGATGCGATCTGTTTTACTGTA
1 ACTGCAACTTCAGTGAGATAAGACTTGTAATTTCAATAAAGTCAGACGCGATCCATTCTACTACA
* * *
28101019 ACTTCAGATAGATAAGGTCCATCATTTTGATCCAT-TCCACTGCAACTTCAGGGAGATAGGACTC
66 AATTCAGAGAGATAAGATCCATCATTTTGA-CC-TCTCCACTGCAACTTCAGGGAGATAGGACTC
28101083 ATATCTTCAACTTGCCCC
129 ATATCTTCAACTTGCCCC
* * *
28101101 ACTGCAACTTTAG-GGGCATAAGACTTGTAATTTTCAATAAAGTCAGACGTGATCCATTCTACTA
1 ACTGCAACTTCAGTGAG-ATAAGACTTGTAA-TTTCAATAAAGTCAGACGCGATCCATTCTACTA
*
28101165 CAAATTCAGAGAGATAAGATCTATCATTTTGACCTGCTCCACTGCAACTTCAGGGAGATAGGACT
64 CAAATTCAGAGAGATAAGATCCATCATTTTGACCT-CTCCACTGCAACTTCAGGGAGATAGGACT
28101230 TATAATTTTC
Statistics
Matches: 111, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
146 3 0.03
147 27 0.24
148 81 0.73
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (146 bp):
ACTGCAACTTCAGTGAGATAAGACTTGTAATTTCAATAAAGTCAGACGCGATCCATTCTACTACA
AATTCAGAGAGATAAGATCCATCATTTTGACCTCTCCACTGCAACTTCAGGGAGATAGGACTCAT
ATCTTCAACTTGCCCC
Found at i:28101230 original size:104 final size:104
Alignment explanation
Indices: 28101099--28101333 Score: 292
Period size: 104 Copynumber: 2.3 Consensus size: 104
28101089 TCAACTTGCC
* * * *
28101099 CCACTGCAACTTTAGGG-GCATAAGACTTGTAATTTTCAATAAAGTCAGACGTGATCCATTCTAC
1 CCACTGCAACTTCAGGGAG-ATAGGACTTATAATTTTCAATAAAGTCAGACGTGATACATTCTAC
* *
28101163 TACAAATTCAGAGAGATAAGATCTATCATTTTGACCTGCT
65 TACAAATTCAGAGAGATAAGATCCATCATTTTGACCCGCT
* * * **
28101203 CCACTGCAACTTCAGGGAGATAGGACTTATAATTTTCAATAAATTCTGATGTGATATGTTCTACT
1 CCACTGCAACTTCAGGGAGATAGGACTTATAATTTTCAATAAAGTCAGACGTGATACATTCTACT
*** * *
28101268 GTTACTTTAGAGAGATAAGATCCATCATTTTGACCCGCT
66 ACAAATTCAGAGAGATAAGATCCATCATTTTGACCCGCT
* *
28101307 CCACTACAACTTCAGGGAAATAGGACT
1 CCACTGCAACTTCAGGGAGATAGGACT
28101334 CGTATCTTCA
Statistics
Matches: 112, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
104 111 0.99
105 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (104 bp):
CCACTGCAACTTCAGGGAGATAGGACTTATAATTTTCAATAAAGTCAGACGTGATACATTCTACT
ACAAATTCAGAGAGATAAGATCCATCATTTTGACCCGCT
Found at i:28101420 original size:44 final size:44
Alignment explanation
Indices: 28101339--28101430 Score: 112
Period size: 44 Copynumber: 2.1 Consensus size: 44
28101329 GGACTCGTAT
* ** * *
28101339 CTTCAACTTGCCCCACTGCAACTTCAGGGGGATAAGGTTAGTGA
1 CTTCAACCTGCCCCACTGCAACTTCAAAGAGACAAGGTTAGTGA
* * *
28101383 CTTCAACCTGCTCTACTGCAACTTCAAAGAGACAAGGTTTGTGA
1 CTTCAACCTGCCCCACTGCAACTTCAAAGAGACAAGGTTAGTGA
28101427 CTTC
1 CTTC
28101431 GCTGATCTGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (44 bp):
CTTCAACCTGCCCCACTGCAACTTCAAAGAGACAAGGTTAGTGA
Found at i:28101739 original size:24 final size:24
Alignment explanation
Indices: 28101703--28101761 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
28101693 ACGGATTGCC
*
28101703 TCCACTGTAATCTTCAAAGTTTAA
1 TCCACTGTAATCTTCAAAGTTCAA
* * *
28101727 TCCGCTGTAATCTTCAAGGTTCAG
1 TCCACTGTAATCTTCAAAGTTCAA
28101751 TCCACTGTAAT
1 TCCACTGTAAT
28101762 TTTGGGACAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.36
Consensus pattern (24 bp):
TCCACTGTAATCTTCAAAGTTCAA
Found at i:28102407 original size:108 final size:107
Alignment explanation
Indices: 28102233--28102437 Score: 284
Period size: 108 Copynumber: 1.9 Consensus size: 107
28102223 GAAAAATGCT
* *
28102233 TGAAAAAGATTATCACAATGACAAGATGAAATTTTATTTAGGGCAAAACTCCAAACAAATAAATT
1 TGAAAAAGATTATCACAATGACAAGATGAAATTTTATTGAGAGCAAAACTCCAAACAAATAAATT
* *
28102298 AATCAGGATAGCAAATTTTGCTAAAATTCAAAGTGAATAAGA
66 AATCAAGATAGCAAATTTTGCTAAAATACAAAGTGAATAAGA
* * * ** * * *
28102340 TGAAAAAGATTATCACAATGGACAAGATGGAATTTTGTTGAGAGCAAAGCTTGAGACGAATAGAT
1 TGAAAAAGATTATCACAAT-GACAAGATGAAATTTTATTGAGAGCAAAACTCCAAACAAATAAAT
*
28102405 TAATCAAGATAGCAAATTTTGCTAGAATACAAA
65 TAATCAAGATAGCAAATTTTGCTAAAATACAAA
28102438 AATGATAATA
Statistics
Matches: 84, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
107 19 0.23
108 65 0.77
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.26
Consensus pattern (107 bp):
TGAAAAAGATTATCACAATGACAAGATGAAATTTTATTGAGAGCAAAACTCCAAACAAATAAATT
AATCAAGATAGCAAATTTTGCTAAAATACAAAGTGAATAAGA
Found at i:28102783 original size:12 final size:12
Alignment explanation
Indices: 28102763--28102812 Score: 77
Period size: 12 Copynumber: 4.3 Consensus size: 12
28102753 GGCCTCTCAT
28102763 TTTTC-TTTTTC
1 TTTTCTTTTTTC
28102774 TTTTCTTTTTTC
1 TTTTCTTTTTTC
*
28102786 TTTT-TTTATTC
1 TTTTCTTTTTTC
28102797 TTTTCTTTTTTC
1 TTTTCTTTTTTC
28102809 TTTT
1 TTTT
28102813 TTCTATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
11 15 0.43
12 20 0.57
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:28102784 original size:7 final size:7
Alignment explanation
Indices: 28102762--28102822 Score: 65
Period size: 7 Copynumber: 8.7 Consensus size: 7
28102752 TGGCCTCTCA
28102762 TTTTTC-
1 TTTTTCT
28102768 TTTTTC-
1 TTTTTCT
28102774 -TTTTCT
1 TTTTTCT
28102780 TTTTTCTT
1 TTTTTC-T
*
28102788 TTTTTAT
1 TTTTTCT
28102795 TCTTTTCT
1 T-TTTTCT
28102803 TTTTTCT
1 TTTTTCT
28102810 TTTTTCT
1 TTTTTCT
28102817 ATTTTT
1 -TTTTT
28102823 TTTAACATTC
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
5 5 0.10
6 6 0.12
7 20 0.42
8 17 0.35
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTCT
Found at i:28102797 original size:23 final size:23
Alignment explanation
Indices: 28102762--28102824 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
28102752 TGGCCTCTCA
*
28102762 TTTTTCTTTTTCTTTTCTTTTTTC
1 TTTTT-TTATTCTTTTCTTTTTTC
28102786 TTTTTTTATTCTTTTCTTTTTTC
1 TTTTTTTATTCTTTTCTTTTTTC
*
28102809 TTTTTTCTATTTTTTT
1 TTTTTT-TATTCTTTT
28102825 TAACATTCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 23 0.64
24 13 0.36
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (23 bp):
TTTTTTTATTCTTTTCTTTTTTC
Found at i:28102810 original size:30 final size:30
Alignment explanation
Indices: 28102765--28102823 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
28102755 CCTCTCATTT
28102765 TTCTTTTTCTTTTCTTTTTTCT-TTTTTTA
1 TTCTTTTTCTTTTCTTTTTTCTATTTTTTA
*
28102794 TTCTTTTCTTTTTTCTTTTTTCTATTTTTT
1 TTCTTTT-TCTTTTCTTTTTTCTATTTTTT
28102824 TTAACATTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 7 0.26
30 14 0.52
31 6 0.22
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (30 bp):
TTCTTTTTCTTTTCTTTTTTCTATTTTTTA
Found at i:28103414 original size:22 final size:20
Alignment explanation
Indices: 28103378--28103436 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
28103368 GGCCCGACCT
28103378 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA--AAAA
28103400 ATTTATTTTAAAAATTAAAAA
1 ATTTATTTTAAAAA-TAAAAA
**
28103421 AAGTATTTTAAAAATA
1 ATTTATTTTAAAAATA
28103437 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 16 0.48
22 7 0.21
23 8 0.24
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTTATTTTAAAAATAAAAA
Found at i:28103438 original size:11 final size:11
Alignment explanation
Indices: 28103418--28103485 Score: 63
Period size: 11 Copynumber: 6.4 Consensus size: 11
28103408 TAAAAATTAA
28103418 AAAAAGTATTTT
1 AAAAA-TATTTT
28103430 AAAAATATTTT
1 AAAAATATTTT
*
28103441 --AAA-A-TTA
1 AAAAATATTTT
* *
28103448 AAAAAAAATTT
1 AAAAATATTTT
28103459 AAAAAGTATTTT
1 AAAAA-TATTTT
28103471 AAAAATATTTT
1 AAAAATATTTT
28103482 AAAA
1 AAAA
28103486 TTAAAAAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
7 2 0.04
8 1 0.02
9 6 0.13
10 1 0.02
11 23 0.49
12 14 0.30
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:28103465 original size:41 final size:41
Alignment explanation
Indices: 28103409--28103541 Score: 182
Period size: 41 Copynumber: 3.3 Consensus size: 41
28103399 AATTTATTTT
28103409 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAA
1 AAAAATT-AAAAAAGTATTTTAAAAATATTTTAAAATTAAAA
*
28103451 AAAAATTTAAAAAGTATTTTAAAAATATTTTAAAATTAAAA
1 AAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAAA
* * *
28103492 AATAA-TAAAAAAGTATTTTAAAAA-A-ATTATAATTAAAA
1 AAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAAA
**
28103530 AAATTTTAAAAA
1 AAAAATTAAAAA
28103542 TAAATATATT
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
38 13 0.16
39 7 0.09
40 18 0.22
41 37 0.45
42 7 0.09
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (41 bp):
AAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAAA
Found at i:28103489 original size:29 final size:30
Alignment explanation
Indices: 28103452--28103514 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
28103442 AAATTAAAAA
* * *
28103452 AAAATTTAAAAAGTATTTTAAAAA-TATTTT
1 AAAATTTAAAAAATA-ATAAAAAAGTATTTT
28103482 AAAA-TTAAAAAATAATAAAAAAGTATTTT
1 AAAATTTAAAAAATAATAAAAAAGTATTTT
28103511 AAAA
1 AAAA
28103515 AAATTATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 6 0.21
29 19 0.66
30 4 0.14
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATTTAAAAAATAATAAAAAAGTATTTT
Found at i:28103523 original size:27 final size:27
Alignment explanation
Indices: 28103471--28103541 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
28103461 AAAGTATTTT
28103471 AAAAATATTTTAAAATTAAAAAATAA-TA
1 AAAAATATTTTAAAA--AAAAAATAATTA
**
28103499 AAAAAGTATTTTAAAAAAATTATAATTA
1 AAAAA-TATTTTAAAAAAAAAATAATTA
28103527 AAAAA-ATTTTAAAAA
1 AAAAATATTTTAAAAA
28103542 TAAATATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
26 10 0.26
27 7 0.18
28 12 0.31
29 10 0.26
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (27 bp):
AAAAATATTTTAAAAAAAAAATAATTA
Found at i:28103549 original size:27 final size:27
Alignment explanation
Indices: 28103469--28103549 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 27
28103459 AAAAAGTATT
* * *
28103469 TTAAAAATATTTTAAAATTAAAAAATAA
1 TTAAAAAAATTTTAAAAAT-AAATATAA
*
28103497 -TAAAAAAGTATTTTAAAAA-AATTATAA
1 TTAAAAAA--ATTTTAAAAATAAATATAA
28103524 TTAAAAAAATTTTAAAAATAAATATA
1 TTAAAAAAATTTTAAAAATAAATATA
28103550 TTTATTATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
26 10 0.23
27 18 0.41
28 7 0.16
29 9 0.20
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (27 bp):
TTAAAAAAATTTTAAAAATAAATATAA
Found at i:28107226 original size:107 final size:107
Alignment explanation
Indices: 28107090--28107365 Score: 453
Period size: 107 Copynumber: 2.6 Consensus size: 107
28107080 GCTAAACGAG
* *
28107090 AAATCGAAACCTAGCGCATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAATATTGCCTTACT
1 AAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAATATTGCCTTACT
* * *
28107155 TTGAAATTTTAAAAGTATATTTGGCTATTTGGTCGAACGAAA
66 TTGAAATTTTAAAAGGATATTTGGCTACTTGGTCAAACGAAA
*
28107197 AAATCGAAACCCAGCACATTAGGGTACGTTTTCTCGAATTTCCAAACGCAAAATATTGCCTTACT
1 AAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAATATTGCCTTACT
28107262 TTGAAATTTTAAAAGGATATTTGGCTACTTGGTCAAACGAAA
66 TTGAAATTTTAAAAGGATATTTGGCTACTTGGTCAAACGAAA
* * * * *
28107304 AAATCAAAACCCGGCACATTAGGGCATGTTTTCTCGAATTTTCAAACGCAAAATATAGCCTT
1 AAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAATATTGCCTT
28107366 TATTATTTTT
Statistics
Matches: 157, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
107 157 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (107 bp):
AAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAATATTGCCTTACT
TTGAAATTTTAAAAGGATATTTGGCTACTTGGTCAAACGAAA
Found at i:28107972 original size:13 final size:13
Alignment explanation
Indices: 28107954--28107979 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28107944 AACAAATTAT
28107954 AAAATATATATAA
1 AAAATATATATAA
28107967 AAAATATATATAA
1 AAAATATATATAA
28107980 GTATGTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATATATATAA
Found at i:28108298 original size:3 final size:3
Alignment explanation
Indices: 28108290--28108355 Score: 100
Period size: 3 Copynumber: 22.7 Consensus size: 3
28108280 AAACTAATAC
28108290 AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
28108337 AAT -AT AAC AAG AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
28108356 AAAAAAGGAC
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
2 4 0.07
3 54 0.93
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:28114395 original size:18 final size:18
Alignment explanation
Indices: 28114374--28114430 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
28114364 ATCCAATCCA
**
28114374 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
28114392 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
28114410 AACCC-A--ACCCAACCC
1 AACCCAAGTACCCAACCC
28114425 AACCCA
1 AACCCA
28114431 TAAAAATTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 14 0.40
17 1 0.03
18 20 0.57
ACGTcount: A:0.40, C:0.49, G:0.02, T:0.09
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:28114396 original size:5 final size:5
Alignment explanation
Indices: 28114386--28114430 Score: 63
Period size: 5 Copynumber: 8.4 Consensus size: 5
28114376 CCCAAGTATT
28114386 CAACC CAACC CAATTACC CAACC CAACC CAACC CAACC CAACC CA
1 CAACC CAACC C-A--ACC CAACC CAACC CAACC CAACC CAACC CA
28114431 TAAAAATTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
5 31 0.84
6 1 0.03
7 1 0.03
8 4 0.11
ACGTcount: A:0.40, C:0.56, G:0.00, T:0.04
Consensus pattern (5 bp):
CAACC
Found at i:28114502 original size:8 final size:8
Alignment explanation
Indices: 28114489--28114523 Score: 70
Period size: 8 Copynumber: 4.4 Consensus size: 8
28114479 AACTAAAACT
28114489 AAAGTCTA
1 AAAGTCTA
28114497 AAAGTCTA
1 AAAGTCTA
28114505 AAAGTCTA
1 AAAGTCTA
28114513 AAAGTCTA
1 AAAGTCTA
28114521 AAA
1 AAA
28114524 ATAATTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.23
Consensus pattern (8 bp):
AAAGTCTA
Found at i:28122562 original size:59 final size:58
Alignment explanation
Indices: 28122499--28122802 Score: 205
Period size: 59 Copynumber: 5.1 Consensus size: 58
28122489 TATAGTATCA
28122499 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAA-AATTTTATTAAAT
* * * * * * * *
28122558 TATA-TAT--TTTAATTATAATAT-ATTTAATAATAATTATGTTGATTTATATTTTA-TAGTAT
1 TATATTATGATTTGAGTA-AAT-TCATATAAGAAT-ATTA-ATT-ATTAAAATTTTATTA-AAT
*
28122617 CATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAATAATTTTATTAAAT
1 --TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAA-AATTTTATTAAAT
* * * * * * * *
28122678 TATATATTTTATTT-A-TAACA-T-ATTTAATAATAATTATGTTAATTTATATTTTA-TAGTAT
1 TATAT-TATGATTTGAGTAA-ATTCATATAAGAAT-ATTA-ATT-ATTAAAATTTTATTA-AAT
*
28122737 CATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
1 --TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAA-AATTTTATTAAAT
28122798 TATAT
1 TATAT
28122803 ATTTTAATTA
Statistics
Matches: 182, Mismatches: 35, Indels: 56
0.67 0.13 0.21
Matches are distributed among these distances:
56 6 0.03
57 19 0.10
58 19 0.10
59 36 0.20
60 28 0.15
61 31 0.17
62 18 0.10
63 19 0.10
64 6 0.03
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (58 bp):
TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAAATTTTATTAAAT
Found at i:28122565 original size:61 final size:60
Alignment explanation
Indices: 28122498--28122805 Score: 244
Period size: 61 Copynumber: 5.1 Consensus size: 60
28122488 TTATAGTATC
28122498 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAA-AATTTTATTAAATT
* * * * * * * * *
28122559 ATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATTATGTTGATTTATATTTTA-TAGTATC
1 ATATATTATGATTTGAGTAAAT-TCATATAAGAAT-ATTA-ATT-ATTAAAATTTTATTA-AATT
*
28122618 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAATAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAA-AATTTTATTAAATT
* * * * * * * *
28122679 ATATATT-TTATTT-A-TAACA-T-ATTTAATAATAATTATGTTAATTTATATTTTA-TAGTATC
1 ATATATTATGATTTGAGTAA-ATTCATATAAGAAT-ATTA-ATT-ATTAAAATTTTATTA-AATT
*
28122738 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAA-AATTTTATTAAATT
28122799 ATATATT
1 ATATATT
28122806 TTAATTATAA
Statistics
Matches: 186, Mismatches: 37, Indels: 48
0.69 0.14 0.18
Matches are distributed among these distances:
57 19 0.10
58 17 0.09
59 37 0.20
60 34 0.18
61 44 0.24
62 16 0.09
63 19 0.10
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.50
Consensus pattern (60 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAAATTTTATTAAATT
Found at i:28122585 original size:15 final size:15
Alignment explanation
Indices: 28122550--28122591 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28122540 TTAAGAATTT
*
28122550 TATTAAATTAT-ATA
1 TATTTAATTATAATA
28122564 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
28122578 TATTTAATAATAAT
1 TATTTAATTATAAT
28122592 TATGTTGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:28122638 original size:120 final size:120
Alignment explanation
Indices: 28122425--28122837 Score: 711
Period size: 120 Copynumber: 3.4 Consensus size: 120
28122415 NNNNATTTTA
* * * * *
28122425 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AATTTATATTT
*
28122489 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
*
28122545 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTGATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
*
28122610 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAT
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
* *
28122665 AATTTTATTAAATTATATATTTTATTTATAACATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
28122730 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
*
28122785 AATTTTATTAAATTATATATTTTAATTATAATATATTTATTAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
28122838 TAAATATGAT
Statistics
Matches: 277, Mismatches: 15, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
120 275 0.99
121 2 0.01
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:28123066 original size:45 final size:44
Alignment explanation
Indices: 28122985--28123075 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
28122975 ACATCTATTC
*
28122985 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
*** *
28123029 CATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCCATTA
1 CATTCAACCAAACACAAGA-TTACTATTACACCTCTATTCCATTA
28123074 CA
1 CA
28123076 CCTCTATTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 16 0.39
45 25 0.61
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
Found at i:28123075 original size:16 final size:16
Alignment explanation
Indices: 28123054--28123123 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
28123044 TTGATTTGCT
*
28123054 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
* *
28123070 ATTACACCTCTATTCT
1 ATTACACCTCTAATCC
28123086 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
28123102 AATACACCTCTAATCC
1 ATTACACCTCTAATCC
*
28123118 AATACA
1 ATTACA
28123124 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.33, C:0.34, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:28123088 original size:32 final size:32
Alignment explanation
Indices: 28123052--28123113 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
28123042 AGTTGATTTG
* *
28123052 CTATTACACCTCTATTCCATTACACCTCTATT
1 CTATTACACCTCTAATCCAATACACCTCTATT
28123084 CTATTACACCTCTAATCCAATACACCTCTA
1 CTATTACACCTCTAATCCAATACACCTCTA
28123114 ATCCAATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (32 bp):
CTATTACACCTCTAATCCAATACACCTCTATT
Found at i:28125978 original size:3 final size:3
Alignment explanation
Indices: 28125972--28126014 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
28125962 GAGAGAAAGG
*
28125972 AGA AGA AG- AGA AGG AGA AGA AGA AGA AGA AGA AGAA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA A
28126015 AAAAGAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:28126208 original size:20 final size:20
Alignment explanation
Indices: 28126183--28126454 Score: 99
Period size: 19 Copynumber: 13.7 Consensus size: 20
28126173 TTTAGATTAG
*
28126183 AATTTTGTATGAATATTTTA
1 AATTTTGTATGAATATTATA
28126203 AATTTTTTGTATGAATATTATA
1 AA--TTTTGTATGAATATTATA
* * *
28126225 ATTTTTTTATGAATATTGT-
1 AATTTTGTATGAATATTATA
* *
28126244 AATGTTGTATGAATATTGTA
1 AATTTTGTATGAATATTATA
* * *
28126264 ATTATTTTATAATTAA-ATT-TG
1 A--ATTTTGT-ATGAATATTATA
* * *
28126285 TATTTATAGTTTTG--GATTAGTA
1 AATTT-T-G-TATGAATATTA-TA
* *
28126307 ATTTTTTGTATGAATATTGT-
1 A-ATTTTGTATGAATATTATA
28126327 AATTTTGTATGAATATTATA
1 AATTTTGTATGAATATTATA
*
28126347 AATTTT-T-TG-----TATG
1 AATTTTGTATGAATATTATA
*
28126360 AATATTGTAAT-AATATTAT-
1 AATTTTGT-ATGAATATTATA
* **
28126379 AGTTTTGTATGAATATTGCA
1 AATTTTGTATGAATATTATA
* *
28126399 ATTTTTTTGTATGAATATTGT-
1 A--ATTTTGTATGAATATTATA
28126420 AATTTTGTATGAATATTATA
1 AATTTTGTATGAATATTATA
**
28126440 TTTTTTTGTATGAAT
1 -AATTTTGTATGAAT
28126455 GTTGTAATAT
Statistics
Matches: 187, Mismatches: 35, Indels: 59
0.67 0.12 0.21
Matches are distributed among these distances:
13 8 0.04
14 1 0.01
16 1 0.01
18 4 0.02
19 65 0.35
20 36 0.19
21 17 0.09
22 48 0.26
23 7 0.04
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.55
Consensus pattern (20 bp):
AATTTTGTATGAATATTATA
Found at i:28126212 original size:22 final size:21
Alignment explanation
Indices: 28126185--28126370 Score: 163
Period size: 22 Copynumber: 9.0 Consensus size: 21
28126175 TAGATTAGAA
*
28126185 TTTTGTATGAATATTTTAAATT
1 TTTTGTATGAATATTGT-AATT
*
28126207 TTTTGTATGAATATTATAATT
1 TTTTGTATGAATATTGTAATT
28126228 TTTT-TATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
*
28126246 TGTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
* *
28126267 ATTTTATAATTAA-ATTTGT-ATT
1 -TTTTGT-ATGAATA-TTGTAATT
* * * * *
28126289 TATAGTTTTGGAT-TAGTAATT
1 TTTTG-TATGAATATTGTAATT
28126310 TTTTGTATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
*
28126329 TTTTGTATGAATATTATAAATT
1 TTTTGTATGAATATTGT-AATT
28126351 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTGTAAT
28126371 AATATTATAG
Statistics
Matches: 131, Mismatches: 20, Indels: 27
0.74 0.11 0.15
Matches are distributed among these distances:
18 3 0.02
19 30 0.23
20 23 0.18
21 26 0.20
22 41 0.31
23 8 0.06
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.55
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:28126334 original size:19 final size:19
Alignment explanation
Indices: 28126310--28126538 Score: 137
Period size: 19 Copynumber: 13.1 Consensus size: 19
28126300 ATTAGTAATT
28126310 TTTTGTATGAATATTGTAA
1 TTTTGTATGAATATTGTAA
*
28126329 TTTTGTATGAATATTATAAA
1 TTTTGTATGAATATTGT-AA
28126349 TTTT-T-TG--TA-TG-AA
1 TTTTGTATGAATATTGTAA
* * *
28126362 TATTGTAAT-AATATTATAG
1 TTTTGT-ATGAATATTGTAA
*
28126381 TTTTGTATGAATATTGCAA
1 TTTTGTATGAATATTGTAA
28126400 TTTTTTTGTATGAATATTGTAA
1 ---TTTTGTATGAATATTGTAA
*
28126422 TTTTGTATGAATATTAT-A
1 TTTTGTATGAATATTGTAA
*
28126440 TTTT-TTTG--TA-TG-AA
1 TTTTGTATGAATATTGTAA
* *
28126454 TGTTG--T-AATATTATAA
1 TTTTGTATGAATATTGTAA
*
28126470 TTTTGTATGAATATTGCAA
1 TTTTGTATGAATATTGTAA
*
28126489 TTTT-TTTG--TA-TG-AA
1 TTTTGTATGAATATTGTAA
*
28126503 TATTG--T-AATATTGTAA
1 TTTTGTATGAATATTGTAA
28126519 TTTTGTATGAATATTGTAA
1 TTTTGTATGAATATTGTAA
28126538 T
1 T
28126539 GTGAGGATAT
Statistics
Matches: 160, Mismatches: 21, Indels: 58
0.67 0.09 0.24
Matches are distributed among these distances:
13 7 0.04
14 15 0.09
15 8 0.05
16 17 0.11
17 5 0.03
18 15 0.09
19 69 0.43
20 6 0.04
22 18 0.11
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.54
Consensus pattern (19 bp):
TTTTGTATGAATATTGTAA
Found at i:28126351 original size:41 final size:40
Alignment explanation
Indices: 28126185--28126370 Score: 175
Period size: 41 Copynumber: 4.5 Consensus size: 40
28126175 TAGATTAGAA
*
28126185 TTTTGTATGAATATTTTAAATTTTTTGTATGAATATTATAATT
1 TTTTGTATGAATATTGT-AA--TTTTGTATGAATATTATAATT
* *
28126228 TTTT-TATGAATATTGTAATGTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATTTTGTATGAATATTATAATT
* * * *
28126267 ATTTTATAATTAA-ATTTGT-ATTTATAGTTTTG--GATTAGTAATT
1 -TTTTGT-ATGAATA-TTGTAATTT-T-G-TATGAATATTA-TAATT
28126310 TTTTGTATGAATATTGTAATTTTGTATGAATATTATAAATT
1 TTTTGTATGAATATTGTAATTTTGTATGAATATTAT-AATT
28126351 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTGTAAT
28126371 AATATTATAG
Statistics
Matches: 118, Mismatches: 12, Indels: 28
0.75 0.08 0.18
Matches are distributed among these distances:
39 22 0.19
40 6 0.05
41 44 0.37
42 33 0.28
43 10 0.08
44 3 0.03
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.55
Consensus pattern (40 bp):
TTTTGTATGAATATTGTAATTTTGTATGAATATTATAATT
Found at i:28126406 original size:22 final size:23
Alignment explanation
Indices: 28126329--28126534 Score: 153
Period size: 22 Copynumber: 8.7 Consensus size: 23
28126319 AATATTGTAA
*
28126329 TTTTGTATGAATATT--ATAAATT
1 TTTTGTATGAATATTGAAT-ATTT
28126351 TTTTGTATGAATATTGTAATAATATTAT
1 TTTTGTATGAATATTG----AATATT-T
*
28126379 AGTTTTGTATGAATATTGCA-ATTT
1 --TTTTGTATGAATATTGAATATTT
*
28126403 TTTTGTATGAATATTG--TA--A
1 TTTTGTATGAATATTGAATATTT
28126422 TTTTGTATGAATATT--ATATTT
1 TTTTGTATGAATATTGAATATTT
*
28126443 TTTTGTATGAATGTTGTAATATTAT
1 TTTTGTATGAATATTG-AATATT-T
*
28126468 AATTTTGTATGAATATTGCA-ATTT
1 --TTTTGTATGAATATTGAATATTT
28126492 TTTTGTATGAATATTGTAATATTGT
1 TTTTGTATGAATATTG-AATATT-T
28126517 AATTTTGTATGAATATTG
1 --TTTTGTATGAATATTG
28126535 TAATGTGAGG
Statistics
Matches: 152, Mismatches: 8, Indels: 43
0.75 0.04 0.21
Matches are distributed among these distances:
19 17 0.11
21 15 0.10
22 47 0.31
23 1 0.01
24 10 0.07
25 8 0.05
26 2 0.01
27 33 0.22
28 3 0.02
30 16 0.11
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.54
Consensus pattern (23 bp):
TTTTGTATGAATATTGAATATTT
Found at i:28126481 original size:27 final size:26
Alignment explanation
Indices: 28126412--28126538 Score: 146
Period size: 27 Copynumber: 5.1 Consensus size: 26
28126402 TTTTTGTATG
28126412 AATATTGTAATTTTGTATGAATA-T-T
1 AATATT-TAATTTTGTATGAATATTGT
*
28126437 -ATATTT--TTTTGTATGAATGTTGT
1 AATATTTAATTTTGTATGAATATTGT
28126460 AATATTATAATTTTGTATGAATATTG-
1 AATATT-TAATTTTGTATGAATATTGT
*
28126486 CA-ATTT--TTTTGTATGAATATTGT
1 AATATTTAATTTTGTATGAATATTGT
28126509 AATATTGTAATTTTGTATGAATATTGT
1 AATATT-TAATTTTGTATGAATATTGT
28126536 AAT
1 AAT
28126539 GTGAGGATAT
Statistics
Matches: 87, Mismatches: 4, Indels: 20
0.78 0.04 0.18
Matches are distributed among these distances:
21 12 0.14
22 17 0.20
23 3 0.03
24 14 0.16
25 5 0.06
26 1 0.01
27 35 0.40
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.54
Consensus pattern (26 bp):
AATATTTAATTTTGTATGAATATTGT
Found at i:28126503 original size:89 final size:91
Alignment explanation
Indices: 28126308--28126517 Score: 352
Period size: 89 Copynumber: 2.3 Consensus size: 91
28126298 GGATTAGTAA
28126308 TTTTTTGTATGAATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATAA
1 TTTTTTGTATGAATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTG--ATAA
*
28126373 TATTATAGTTTTGTATGAATATTGCAAT
64 TATTATAATTTTGTATGAATATTGCAAT
* *
28126401 TTTTTTGTATGAATATTGTAATTTTGTATGAATATTAT-ATTTTTTTGTATGAATGTTG-TAATA
1 TTTTTTGTATGAATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGATAATA
28126464 TTATAATTTTGTATGAATATTGCAAT
66 TTATAATTTTGTATGAATATTGCAAT
*
28126490 TTTTTTGTATGAATATTGTAATATTGTA
1 TTTTTTGTATGAATATTGTAATTTTGTA
28126518 ATTTTGTATG
Statistics
Matches: 113, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
89 57 0.50
92 18 0.16
93 38 0.34
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.54
Consensus pattern (91 bp):
TTTTTTGTATGAATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGATAATA
TTATAATTTTGTATGAATATTGCAAT
Found at i:28126511 original size:49 final size:49
Alignment explanation
Indices: 28126319--28126534 Score: 251
Period size: 49 Copynumber: 4.5 Consensus size: 49
28126309 TTTTTGTATG
*
28126319 AATATTGTAATTTTGTATGAATATT-ATAAATTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGAT-ATTTTTTTGTATGAATATTGT
28126368 AATAATAT-TATAGTTTTGTATGAATATTGCA-A--TTTTT-T-TG--TA-TG-
1 AAT-AT-TGTA-A-TTTTGTATGAATATTG-ATATTTTTTTGTATGAATATTGT
*
28126412 AATATTGTAATTTTGTATGAATATT-ATATTTTTTTGTATGAATGTTGT
1 AATATTGTAATTTTGTATGAATATTGATATTTTTTTGTATGAATATTGT
*
28126460 AATATTATAATTTTGTATGAATATTGCA-ATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTG-ATATTTTTTTGTATGAATATTGT
28126509 AATATTGTAATTTTGTATGAATATTG
1 AATATTGTAATTTTGTATGAATATTG
28126535 TAATGTGAGG
Statistics
Matches: 145, Mismatches: 4, Indels: 36
0.78 0.02 0.19
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 15 0.10
42 7 0.05
43 5 0.03
44 5 0.03
45 2 0.01
46 3 0.02
47 2 0.01
48 26 0.18
49 49 0.34
50 10 0.07
51 2 0.01
52 16 0.11
54 1 0.01
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.53
Consensus pattern (49 bp):
AATATTGTAATTTTGTATGAATATTGATATTTTTTTGTATGAATATTGT
Found at i:28126517 original size:41 final size:41
Alignment explanation
Indices: 28126383--28126517 Score: 157
Period size: 40 Copynumber: 3.1 Consensus size: 41
28126373 TATTATAGTT
*
28126383 TTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATT
1 TTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATA
*
28126424 TTGTATGAATATT--ATATTTTTTTGTATGAATGTTGTAATATTATAA
1 TTGTATGAATATTGCA-ATTTTTTTGTATGAATATTG---TA--AT-A
28126470 TTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATA
1 --TTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATA
28126513 TTGTA
1 TTGTA
28126518 ATTTTGTATG
Statistics
Matches: 80, Mismatches: 3, Indels: 22
0.76 0.03 0.21
Matches are distributed among these distances:
39 1 0.01
40 19 0.24
41 18 0.22
43 3 0.04
44 2 0.03
45 2 0.03
46 2 0.03
48 13 0.16
49 19 0.24
50 1 0.01
ACGTcount: A:0.30, C:0.01, G:0.14, T:0.54
Consensus pattern (41 bp):
TTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATA
Found at i:28126779 original size:38 final size:38
Alignment explanation
Indices: 28126734--28126807 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
28126724 CATATAAAGT
28126734 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
*
28126772 TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTT
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTT
28126808 GGGTTTTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (38 bp):
TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
Found at i:28128594 original size:6 final size:6
Alignment explanation
Indices: 28128583--28128683 Score: 184
Period size: 6 Copynumber: 16.8 Consensus size: 6
28128573 GCATCATGCA
*
28128583 CCAGAG CCAGAG CCAGAG CCAGGG CCAGAG CCAGAG CCAGAG CCAGAG
1 CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG
28128631 CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG
1 CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG
*
28128679 GCAGA
1 CCAGA
28128684 ACTACATTCT
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 92 1.00
ACGTcount: A:0.33, C:0.33, G:0.35, T:0.00
Consensus pattern (6 bp):
CCAGAG
Found at i:28131402 original size:22 final size:21
Alignment explanation
Indices: 28131341--28131414 Score: 93
Period size: 22 Copynumber: 3.6 Consensus size: 21
28131331 NTATTACAAC
28131341 ATTCATACAAAAAAATAT-AAT
1 ATTCATACAAAAAAAT-TCAAT
28131362 ATTCATAC---AAAATTACAAT
1 ATTCATACAAAAAAATT-CAAT
28131381 ATTCATACAAAAAAATTGCAAT
1 ATTCATACAAAAAAATT-CAAT
28131403 ATTCATACAAAA
1 ATTCATACAAAA
28131415 CTATAATATT
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
17 1 0.02
18 5 0.11
19 11 0.23
21 8 0.17
22 22 0.47
ACGTcount: A:0.57, C:0.14, G:0.01, T:0.28
Consensus pattern (21 bp):
ATTCATACAAAAAAATTCAAT
Found at i:28131406 original size:41 final size:40
Alignment explanation
Indices: 28131333--28131590 Score: 186
Period size: 41 Copynumber: 6.1 Consensus size: 40
28131323 NNNNNNNNNT
*
28131333 ATTACAACATTCATACAAAAAAATATAATATTCATACAAA
1 ATTACAATATTCATACAAAAAAATATAATATTCATACAAA
28131373 ATTACAATATTCATACAAAAAAAT-TGCAATATTCATACAAAACTATAATA
1 ATTACAATATTCATACAAAAAAATAT--AATATTCAT-----AC---AA-A
*
28131423 TTATTACAATATTCATACAAAAAATTTATAATATTCATACAAA
1 --ATTACAATATTCATACAAAAAA-ATATAATATTCATACAAA
* * *
28131466 ATTACAATATTCATAC-AAAAAAT-TACTAATCCAAAACTATAA
1 ATTACAATATTCATACAAAAAAATATAAT-ATTC-ATAC-A-AA
* * * * *
28131508 A-TACAA-ATTTAATTATAAAATAATTACAATATTCATACAAC
1 ATTACAATA-TTCA-TACAAAA-AAATATAATATTCATACAAA
*
28131549 ATTACAATATTCATA-AAAAAATTATAATATTCATACAAA
1 ATTACAATATTCATACAAAAAAATATAATATTCATACAAA
28131588 ATT
1 ATT
28131591 CTAATCTAAA
Statistics
Matches: 175, Mismatches: 17, Indels: 53
0.71 0.07 0.22
Matches are distributed among these distances:
38 3 0.02
39 26 0.15
40 36 0.21
41 38 0.22
42 14 0.08
43 8 0.05
44 8 0.05
45 2 0.01
46 2 0.01
47 2 0.01
49 2 0.01
50 1 0.01
52 31 0.18
53 1 0.01
54 1 0.01
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.32
Consensus pattern (40 bp):
ATTACAATATTCATACAAAAAAATATAATATTCATACAAA
Found at i:28131455 original size:22 final size:22
Alignment explanation
Indices: 28131426--28131588 Score: 102
Period size: 20 Copynumber: 7.9 Consensus size: 22
28131416 TATAATATTA
28131426 TTACAATATTCATACAAAAAAT
1 TTACAATATTCATACAAAAAAT
*
28131448 TTATAATATTCATAC--AAAA-
1 TTACAATATTCATACAAAAAAT
28131467 TTACAATATTCATACAAAAAA-
1 TTACAATATTCATACAAAAAAT
* * * * *
28131488 TTACTA-ATCCAAAACTATAAA-
1 TTACAATATTC-ATACAAAAAAT
* *
28131509 -TACAA-ATTTAATTATAAAATAA-
1 TTACAATA-TTCA-TACAAAA-AAT
*
28131531 TTACAATATTCATAC--AACA-
1 TTACAATATTCATACAAAAAAT
28131550 TTACAATATTCATA-AAAAAA-
1 TTACAATATTCATACAAAAAAT
*
28131570 TTATAATATTCATACAAAA
1 TTACAATATTCATACAAAA
28131589 TTCTAATCTA
Statistics
Matches: 111, Mismatches: 19, Indels: 23
0.73 0.12 0.15
Matches are distributed among these distances:
19 29 0.26
20 31 0.28
21 24 0.22
22 18 0.16
23 8 0.07
24 1 0.01
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.33
Consensus pattern (22 bp):
TTACAATATTCATACAAAAAAT
Found at i:28131483 original size:52 final size:52
Alignment explanation
Indices: 28131373--28131476 Score: 163
Period size: 52 Copynumber: 2.0 Consensus size: 52
28131363 TTCATACAAA
* *
28131373 ATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAACTATAATATT
1 ATTACAATATTCATACAAAAAAATTACAATATTCATACAAAACTACAATATT
* * *
28131425 ATTACAATATTCATACAAAAAATTTATAATATTCATACAAAATTACAATATT
1 ATTACAATATTCATACAAAAAAATTACAATATTCATACAAAACTACAATATT
28131477 CATACAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.35
Consensus pattern (52 bp):
ATTACAATATTCATACAAAAAAATTACAATATTCATACAAAACTACAATATT
Found at i:28131595 original size:19 final size:19
Alignment explanation
Indices: 28131333--28131590 Score: 149
Period size: 19 Copynumber: 13.2 Consensus size: 19
28131323 NNNNNNNNNT
*
28131333 ATTACAACATTCATACAAAAA
1 ATTACAATATTCATAC--AAA
* *
28131354 AATATAATATTCATACAAA
1 ATTACAATATTCATACAAA
28131373 ATTACAATATTCATACAAAAAA
1 ATTACAATATTCATAC---AAA
*
28131395 ATTGCAATATTCATACAAA
1 ATTACAATATTCATACAAA
* * *
28131414 ACTATAATATT-ATTACAAT
1 ATTACAATATTCA-TACAAA
28131433 ATT-C-ATA--CA-A-AAA
1 ATTACAATATTCATACAAA
*
28131446 ATTTATAATATTCATACAAA
1 A-TTACAATATTCATACAAA
28131466 ATTACAATATTCATACAAAAA
1 ATTACAATATTCATAC--AAA
* * *
28131487 ATTACTA-ATCCAAAACTATAA
1 ATTACAATATTC-ATAC-A-AA
*
28131508 A-TACAAATTTAATT-ATAAAATA
1 ATTAC-AA--T-ATTCATACAA-A
*
28131530 ATTACAATATTCATACAAC
1 ATTACAATATTCATACAAA
*
28131549 ATTACAATATTCATAAAAAA
1 ATTACAATATTCAT-ACAAA
*
28131569 ATTATAATATTCATACAAA
1 ATTACAATATTCATACAAA
28131588 ATT
1 ATT
28131591 CTAATCTAAA
Statistics
Matches: 183, Mismatches: 29, Indels: 52
0.69 0.11 0.20
Matches are distributed among these distances:
13 3 0.02
14 3 0.02
16 4 0.02
17 3 0.02
18 3 0.02
19 74 0.40
20 33 0.18
21 30 0.16
22 23 0.13
23 5 0.03
25 2 0.01
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
ATTACAATATTCATACAAA
Found at i:28131766 original size:3 final size:3
Alignment explanation
Indices: 28131758--28131801 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
28131748 TTTTCTTTCT
* *
28131758 TTC TTC TTC TTC TTC -TC TTC TTC TTC TTC -TC CTC CTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
28131802 CCTTTCTCTC
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (3 bp):
TTC
Found at i:28131776 original size:14 final size:14
Alignment explanation
Indices: 28131754--28131802 Score: 73
Period size: 14 Copynumber: 3.6 Consensus size: 14
28131744 CATTTTTTCT
28131754 TTCTT-TCTTCTTC
1 TTCTTCTCTTCTTC
28131767 TTCTTCTCTTCTTC
1 TTCTTCTCTTCTTC
* *
28131781 TTCTTCTCCTCCTC
1 TTCTTCTCTTCTTC
28131795 TTCTTCTC
1 TTCTTCTC
28131803 CTTTCTCTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
13 5 0.15
14 28 0.85
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (14 bp):
TTCTTCTCTTCTTC
Found at i:28131778 original size:17 final size:17
Alignment explanation
Indices: 28131754--28131801 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
28131744 CATTTTTTCT
28131754 TTCT-TTCTTCTTCTTC
1 TTCTCTTCTTCTTCTTC
28131770 TTCTCTTCTTCTTCTTC
1 TTCTCTTCTTCTTCTTC
* *
28131787 TCCTCCTCTTCTTCT
1 TTCTCTTCTTCTTCT
28131802 CCTTTCTCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 4 0.14
17 25 0.86
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (17 bp):
TTCTCTTCTTCTTCTTC
Found at i:28131803 original size:11 final size:11
Alignment explanation
Indices: 28131762--28131808 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
28131752 CTTTCTTTCT
*
28131762 TCTTCTTCTTC
1 TCTTCTTCTCC
28131773 TCTTCTTCT--
1 TCTTCTTCTCC
*
28131782 TCTTCTCCTCC
1 TCTTCTTCTCC
28131793 TCTTCTTCTCC
1 TCTTCTTCTCC
28131804 T-TTCT
1 TCTTCT
28131809 CTCTTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
9 8 0.25
10 4 0.12
11 20 0.62
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (11 bp):
TCTTCTTCTCC
Found at i:28131812 original size:17 final size:16
Alignment explanation
Indices: 28131756--28131813 Score: 66
Period size: 17 Copynumber: 3.6 Consensus size: 16
28131746 TTTTTTCTTT
*
28131756 CTTTCTTCTTCTTCTT
1 CTTTCTTCTTCTTCTC
28131772 CTCTTCTTCTTCTTCTC
1 CT-TTCTTCTTCTTCTC
*
28131789 C--TCCTCTTCTTCTC
1 CTTTCTTCTTCTTCTC
28131803 CTTTCTCTCTT
1 CTTTCT-TCTT
28131814 TTTTTTTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
14 13 0.37
16 4 0.11
17 18 0.51
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (16 bp):
CTTTCTTCTTCTTCTC
Found at i:28131813 original size:14 final size:13
Alignment explanation
Indices: 28131764--28131813 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 13
28131754 TTCTTTCTTC
*
28131764 TTCTTCTTCTCTT
1 TTCTTCTTCTCCT
28131777 CTTCTTCTTCTCCT
1 -TTCTTCTTCTCCT
*
28131791 CCTCTTCTTCTCCT
1 -TTCTTCTTCTCCT
28131805 TTCTCTCTT
1 TTCT-TCTT
28131814 TTTTTTTCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
13 3 0.09
14 29 0.91
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (13 bp):
TTCTTCTTCTCCT
Found at i:28134272 original size:19 final size:21
Alignment explanation
Indices: 28134235--28134274 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28134225 AAAACATTAT
28134235 TAAAATTCATAAAATATTAAA
1 TAAAATTCATAAAATATTAAA
*
28134256 TAAAGTTCA-AAAA-ATTAAA
1 TAAAATTCATAAAATATTAAA
28134275 AACTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 4 0.22
21 8 0.44
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (21 bp):
TAAAATTCATAAAATATTAAA
Found at i:28144781 original size:18 final size:19
Alignment explanation
Indices: 28144760--28144798 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28144750 AATTTTGGAA
*
28144760 TTTATAAAT-ATTTTGATT
1 TTTAAAAATCATTTTGATT
*
28144778 TTTAAAAATCATTTTTATT
1 TTTAAAAATCATTTTGATT
28144797 TT
1 TT
28144799 ATTTTTTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTAAAAATCATTTTGATT
Found at i:28148024 original size:24 final size:23
Alignment explanation
Indices: 28147992--28148052 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
28147982 ACATAGACAA
*
28147992 AAACTGATACTTCCCTGAAAGTGG
1 AAACTGATACTTCCCAG-AAGTGG
*
28148016 AAACTGATACTTCCCAGAGGTGG
1 AAACTGATACTTCCCAGAAGTGG
* *
28148039 AAATTGAAACTTCC
1 AAACTGATACTTCC
28148053 TAAGGGATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
23 17 0.52
24 16 0.48
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (23 bp):
AAACTGATACTTCCCAGAAGTGG
Found at i:28149017 original size:16 final size:16
Alignment explanation
Indices: 28148971--28149017 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
28148961 AACGAACTAC
*
28148971 TAGAGAAAGGGCAGAA
1 TAGAGAAAGGACAGAA
* *
28148987 GAAAGAAAGGA-AGAA
1 TAGAGAAAGGACAGAA
*
28149002 TAGAGAAAAGACAGAA
1 TAGAGAAAGGACAGAA
28149018 AAAAGAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.60, C:0.04, G:0.32, T:0.04
Consensus pattern (16 bp):
TAGAGAAAGGACAGAA
Found at i:28157681 original size:14 final size:14
Alignment explanation
Indices: 28157662--28157690 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28157652 CATGCTTACT
28157662 CATAATTCATTTTA
1 CATAATTCATTTTA
28157676 CATAATTCATTTTA
1 CATAATTCATTTTA
28157690 C
1 C
28157691 GCATAACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.48
Consensus pattern (14 bp):
CATAATTCATTTTA
Found at i:28157695 original size:16 final size:15
Alignment explanation
Indices: 28157657--28157696 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 15
28157647 CATGACATGC
28157657 TTACTCATAATTCATT
1 TTAC-CATAATTCATT
28157673 TTA-CATAATTCATT
1 TTACCATAATTCATT
28157687 TTACGCATAA
1 TTAC-CATAA
28157697 CATAACTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 14 0.64
16 8 0.36
ACGTcount: A:0.35, C:0.17, G:0.03, T:0.45
Consensus pattern (15 bp):
TTACCATAATTCATT
Found at i:28163491 original size:16 final size:16
Alignment explanation
Indices: 28163447--28163497 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
28163437 TTTGACTTTT
*
28163447 TAAAATTTAT-ATTTA
1 TAAATTTTATAATTTA
* * *
28163462 TATATTTCAGAATTTA
1 TAAATTTTATAATTTA
28163478 TAAATTTTATAATTTTA
1 TAAATTTTATAA-TTTA
28163495 TAA
1 TAA
28163498 TTAATTATTT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
15 6 0.22
16 14 0.52
17 7 0.26
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (16 bp):
TAAATTTTATAATTTA
Found at i:28163682 original size:21 final size:22
Alignment explanation
Indices: 28163650--28163690 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
28163640 GTCAAAGTCA
28163650 AATGTGTTTTTAATTTAAATTT
1 AATGTGTTTTTAATTTAAATTT
*
28163672 AATGT-TTTTTATTTTAAAT
1 AATGTGTTTTTAATTTAAAT
28163691 AAGCTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
AATGTGTTTTTAATTTAAATTT
Found at i:28174170 original size:2 final size:2
Alignment explanation
Indices: 28174163--28174187 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28174153 TACTATGAGT
28174163 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
28174188 TTTCATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:28179399 original size:167 final size:167
Alignment explanation
Indices: 28179123--28179460 Score: 676
Period size: 167 Copynumber: 2.0 Consensus size: 167
28179113 GGCACAAGGC
28179123 AGGCACGGCTAGGTGCACGCCTTGACAGCACTGTTTTCTGTTTGTTGGGCCAAGATCAGGTTCAA
1 AGGCACGGCTAGGTGCACGCCTTGACAGCACTGTTTTCTGTTTGTTGGGCCAAGATCAGGTTCAA
28179188 CGGGTGAGAAGATGCTCAAAGGGGATTGGCCGGGATTTGCTTCATGCCTGTTCTATTCAAAGCTC
66 CGGGTGAGAAGATGCTCAAAGGGGATTGGCCGGGATTTGCTTCATGCCTGTTCTATTCAAAGCTC
28179253 AACATTTGTTGTTTTTGAACTTGGCAGTCAGGTTAAT
131 AACATTTGTTGTTTTTGAACTTGGCAGTCAGGTTAAT
28179290 AGGCACGGCTAGGTGCACGCCTTGACAGCACTGTTTTCTGTTTGTTGGGCCAAGATCAGGTTCAA
1 AGGCACGGCTAGGTGCACGCCTTGACAGCACTGTTTTCTGTTTGTTGGGCCAAGATCAGGTTCAA
28179355 CGGGTGAGAAGATGCTCAAAGGGGATTGGCCGGGATTTGCTTCATGCCTGTTCTATTCAAAGCTC
66 CGGGTGAGAAGATGCTCAAAGGGGATTGGCCGGGATTTGCTTCATGCCTGTTCTATTCAAAGCTC
28179420 AACATTTGTTGTTTTTGAACTTGGCAGTCAGGTTAAT
131 AACATTTGTTGTTTTTGAACTTGGCAGTCAGGTTAAT
28179457 AGGC
1 AGGC
28179461 TTGAAGGTGA
Statistics
Matches: 171, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
167 171 1.00
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (167 bp):
AGGCACGGCTAGGTGCACGCCTTGACAGCACTGTTTTCTGTTTGTTGGGCCAAGATCAGGTTCAA
CGGGTGAGAAGATGCTCAAAGGGGATTGGCCGGGATTTGCTTCATGCCTGTTCTATTCAAAGCTC
AACATTTGTTGTTTTTGAACTTGGCAGTCAGGTTAAT
Found at i:28181472 original size:3 final size:3
Alignment explanation
Indices: 28181464--28181499 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
28181454 AGTCTTTGCT
28181464 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28181500 ATTTCATTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28183258 original size:30 final size:30
Alignment explanation
Indices: 28183194--28183260 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
28183184 TTTTACTTTT
* *
28183194 CCCCCAATACTTTTACTCCCTCCCACTTTC
1 CCCCCAATAATTTTACTCCCTCCCACTCTC
* *
28183224 CCCCCAA-AATTTTACTCCTCTCTCATCTCAC
1 CCCCCAATAATTTTACTCC-CTCCCA-CTCTC
28183255 CCCCCA
1 CCCCCA
28183261 TTTACCCCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 10 0.32
30 12 0.39
31 9 0.29
ACGTcount: A:0.19, C:0.51, G:0.00, T:0.30
Consensus pattern (30 bp):
CCCCCAATAATTTTACTCCCTCCCACTCTC
Found at i:28186114 original size:44 final size:44
Alignment explanation
Indices: 28186058--28186145 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 44
28186048 GAAACAGAAA
* *
28186058 CAGAGCATATCAAGTACTGATGCAGAGCATATCT-GATACAGATG
1 CAGAGCATATCAAATACAGATGCAGAGCATAT-TAGATACAGATG
* *
28186102 CAGAGCATATCAAATACAGATGCGGAGTATATTAGATACAGATG
1 CAGAGCATATCAAATACAGATGCAGAGCATATTAGATACAGATG
28186146 TAAAATCCTA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 1 0.03
44 38 0.97
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.23
Consensus pattern (44 bp):
CAGAGCATATCAAATACAGATGCAGAGCATATTAGATACAGATG
Found at i:28186140 original size:22 final size:22
Alignment explanation
Indices: 28186044--28186145 Score: 107
Period size: 22 Copynumber: 4.6 Consensus size: 22
28186034 AGATTTTAGA
* **
28186044 ATCAGAAACAGAAACAGAGCAT
1 ATCAGATACAGATGCAGAGCAT
*
28186066 ATCA-AGTACTGATGCAGAGCAT
1 ATCAGA-TACAGATGCAGAGCAT
*
28186088 ATCTGATACAGATGCAGAGCAT
1 ATCAGATACAGATGCAGAGCAT
* * *
28186110 ATCAAATACAGATGCGGAGTAT
1 ATCAGATACAGATGCAGAGCAT
*
28186132 ATTAGATACAGATG
1 ATCAGATACAGATG
28186146 TAAAATCCTA
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
21 1 0.02
22 64 0.97
23 1 0.02
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.21
Consensus pattern (22 bp):
ATCAGATACAGATGCAGAGCAT
Found at i:28186702 original size:42 final size:42
Alignment explanation
Indices: 28186646--28186728 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
28186636 CCTCACACTG
* * *
28186646 CCTGGCACAAGGCCGTGTGACTCAAGTCAGTGAGTTACACAT
1 CCTGACACAAGGCCGTGTAACTCAAGTCAGTGACTTACACAT
* *
28186688 CCTGACACATGGCCGTGTAACTTAAGTCAGTGACTTACACA
1 CCTGACACAAGGCCGTGTAACTCAAGTCAGTGACTTACACA
28186729 AGTTGTGCAC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.23
Consensus pattern (42 bp):
CCTGACACAAGGCCGTGTAACTCAAGTCAGTGACTTACACAT
Found at i:28189553 original size:18 final size:17
Alignment explanation
Indices: 28189526--28189560 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
28189516 GCTACAGTAA
28189526 TTAACCATTTTAATTTAG
1 TTAACCA-TTTAATTTAG
*
28189544 TTAACTATTTAATTTAG
1 TTAACCATTTAATTTAG
28189561 CAATACTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (17 bp):
TTAACCATTTAATTTAG
Found at i:28190398 original size:2 final size:2
Alignment explanation
Indices: 28190391--28190416 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28190381 AAATCTTGTA
28190391 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
28190417 TAGAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28192428 original size:2 final size:2
Alignment explanation
Indices: 28192421--28192454 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
28192411 TATTTATACT
28192421 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28192455 TACTATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:28192590 original size:22 final size:22
Alignment explanation
Indices: 28192551--28192612 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
28192541 GTTATTACTA
28192551 TTATAT-TTATT-TATATATCT
1 TTATATCTTATTATATATATCT
28192571 TTATATCTTATTATATATATCT
1 TTATATCTTATTATATATATCT
*
28192593 ATATATCTTATTATATATAT
1 TTATATCTTATTATATATAT
28192613 ATGTATATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
20 6 0.15
21 5 0.13
22 28 0.72
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATATCTTATTATATATATCT
Found at i:28192619 original size:8 final size:8
Alignment explanation
Indices: 28192562--28192632 Score: 58
Period size: 8 Copynumber: 9.1 Consensus size: 8
28192552 TATATTTATT
28192562 TATATATC
1 TATATATC
*
28192570 TTTATATC
1 TATATATC
*
28192578 T-TAT-TA
1 TATATATC
28192584 TATATATC
1 TATATATC
28192592 TATATATC
1 TATATATC
*
28192600 T-TATTATA
1 TATA-TATC
*
28192608 TATATATG
1 TATATATC
*
28192616 TATATATA
1 TATATATC
*
28192624 TACATATC
1 TATATATC
28192632 T
1 T
28192633 CTTTATAAAC
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
6 2 0.04
7 8 0.16
8 39 0.76
9 2 0.04
ACGTcount: A:0.37, C:0.08, G:0.01, T:0.54
Consensus pattern (8 bp):
TATATATC
Found at i:28192623 original size:12 final size:11
Alignment explanation
Indices: 28192549--28192625 Score: 63
Period size: 10 Copynumber: 7.2 Consensus size: 11
28192539 TTGTTATTAC
*
28192549 TATTATATTTA
1 TATTATATATA
*
28192560 T-TTATATATC
1 TATTATATATA
*
28192570 T-TTATATCT-
1 TATTATATATA
28192579 TATTATATATA
1 TATTATATATA
* *
28192590 T-CTATATATCT
1 TATTATATAT-A
28192601 TATTATATATA
1 TATTATATATA
28192612 TATGTATATATA
1 TAT-TATATATA
28192624 TA
1 TA
28192626 CATATCTCTT
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
9 1 0.02
10 29 0.55
11 6 0.11
12 17 0.32
ACGTcount: A:0.36, C:0.05, G:0.01, T:0.57
Consensus pattern (11 bp):
TATTATATATA
Found at i:28196097 original size:18 final size:18
Alignment explanation
Indices: 28196061--28196099 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
28196051 GATGAAAATG
* *
28196061 ATAACAATAATAATGATA
1 ATAACAATAACAATAATA
*
28196079 ATAACAATAACATTAATA
1 ATAACAATAACAATAATA
28196097 ATA
1 ATA
28196100 TTAATAATGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.28
Consensus pattern (18 bp):
ATAACAATAACAATAATA
Found at i:28196340 original size:6 final size:5
Alignment explanation
Indices: 28196310--28196339 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
28196300 GTTTTTTTAA
28196310 AAAAT AAAAT AAAAT AAAAT AAAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT -AAAAT AAAA
28196340 AAGTGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:28197711 original size:12 final size:12
Alignment explanation
Indices: 28197694--28197720 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28197684 AATAAATCAT
28197694 ATATGTATATTA
1 ATATGTATATTA
28197706 ATATGTATATTA
1 ATATGTATATTA
28197718 ATA
1 ATA
28197721 GAAAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (12 bp):
ATATGTATATTA
Found at i:28198105 original size:21 final size:21
Alignment explanation
Indices: 28198081--28198133 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
28198071 CATTGTTTCT
*
28198081 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
28198102 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
28198123 AATCTCACCGC
1 AATCTCACCGC
28198134 CACCGCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:28198888 original size:21 final size:21
Alignment explanation
Indices: 28198864--28198916 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
28198854 CATTGTTTCT
*
28198864 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
28198885 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
28198906 AATCTCACCGC
1 AATCTCACCGC
28198917 CATCGCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:28199059 original size:21 final size:21
Alignment explanation
Indices: 28199033--28199085 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
28199023 AGTGGTGGCG
*
28199033 GTGAGATTAGTTACTGTAGCA
1 GTGAGATTAGATACTGTAGCA
* *
28199054 GTGAGATTGGATACTGTAGCG
1 GTGAGATTAGATACTGTAGCA
28199075 GTGAGATTAGA
1 GTGAGATTAGA
28199086 AACAATGGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.08, G:0.34, T:0.30
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAGCA
Found at i:28200262 original size:16 final size:16
Alignment explanation
Indices: 28200241--28200273 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
28200231 GGGTATAGGA
28200241 ATTAGTGTTTCAATCT
1 ATTAGTGTTTCAATCT
28200257 ATTAGTGTTTCAATCT
1 ATTAGTGTTTCAATCT
28200273 A
1 A
28200274 CTCCACTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.48
Consensus pattern (16 bp):
ATTAGTGTTTCAATCT
Found at i:28200815 original size:190 final size:189
Alignment explanation
Indices: 28200342--28200865 Score: 735
Period size: 190 Copynumber: 2.8 Consensus size: 189
28200332 CAAGGAAATA
* * * * * *
28200342 AGATTTGTAACTCGCAGCTTTAATTTGTTCCACTGCAACTTCAGGGAAATAAGATTTGC-ATCTC
1 AGATTTGTGACTTGTAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATGAGATTTGCTATCTT
* * * * * *
28200406 CAATCTGCTCCATTACGACTTCAGGGAGATAAGATTGGTGGCTTCAATCTGCCCCACTGCAACTT
66 CAATTTGCTCCACTACAACTTCAGGGAGATGAGATTGGTGGCTTCAATCAGCCCCACTACAACTT
*
28200471 TAAAGAGATAAGATTCGCCATGGTAGATTTAGTCCGACCTACTACAACTCTAAAGGTAT
131 TAAAGAGATAAGATTCGCCATGGTAGATTTAATCCGACCTACTACAACTCTAAAGGTAT
* * *
28200530 AGATTTGTGACTTGTAACTTTAATCTGTTCCACTTCAACTTCAGGGAAATGAGATTCGCTATCTT
1 AGATTTGTGACTTGTAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATGAGATTTGCTATCTT
* * * ** *
28200595 CAATTTGCTCTACTAAAACTTCAGGGAGATGAGATTGGTGGCTTTAATCAGTTCTACTACAACTT
66 CAATTTGCTCCACTACAACTTCAGGGAGATGAGATTGGTGGCTTCAATCAGCCCCACTACAACTT
*
28200660 TAAGGAGATAAGATTCGCCATGGTAGATTTAATCCGACCTACTACAACTCTAAAGGTAT
131 TAAAGAGATAAGATTCGCCATGGTAGATTTAATCCGACCTACTACAACTCTAAAGGTAT
* * *
28200719 AGGATTTGTGACTTGTAGCTTTAATCTGTTCTAATGCAACTTCACGGAAATGAGATTTGCTATCT
1 A-GATTTGTGACTTGTAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATGAGATTTGCTATCT
* * * * *
28200784 TCAATTTGCTCCACTGCAACTTCAAGGAGATGAGATTTGTGGCTTCAATCTGCCCCACTGCAACT
65 TCAATTTGCTCCACTACAACTTCAGGGAGATGAGATTGGTGGCTTCAATCAGCCCCACTACAACT
* *
28200849 TCAGAGAGATAAGATTC
130 TTAAAGAGATAAGATTC
28200866 ACTACTATGA
Statistics
Matches: 291, Mismatches: 43, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
188 51 0.18
189 115 0.40
190 125 0.43
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (189 bp):
AGATTTGTGACTTGTAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATGAGATTTGCTATCTT
CAATTTGCTCCACTACAACTTCAGGGAGATGAGATTGGTGGCTTCAATCAGCCCCACTACAACTT
TAAAGAGATAAGATTCGCCATGGTAGATTTAATCCGACCTACTACAACTCTAAAGGTAT
Found at i:28200845 original size:44 final size:45
Alignment explanation
Indices: 28200753--28200864 Score: 138
Period size: 44 Copynumber: 2.5 Consensus size: 45
28200743 TCTGTTCTAA
* * * * *
28200753 TGCAACTTCACGGAAATGAGATTTGCTATCTTCAATTTGCTCCAC
1 TGCAACTTCAAGGAGATGAGATTTGCTAGCTTCAATCTGCCCCAC
*
28200798 TGCAACTTCAAGGAGATGAGATTTG-TGGCTTCAATCTGCCCCAC
1 TGCAACTTCAAGGAGATGAGATTTGCTAGCTTCAATCTGCCCCAC
*
28200842 TGCAACTTC-AGAGAGATAAGATT
1 TGCAACTTCAAG-GAGATGAGATT
28200865 CACTACTATG
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
43 2 0.03
44 34 0.58
45 23 0.39
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (45 bp):
TGCAACTTCAAGGAGATGAGATTTGCTAGCTTCAATCTGCCCCAC
Found at i:28205195 original size:44 final size:44
Alignment explanation
Indices: 28205132--28205219 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
28205122 TAATCCTGAG
28205132 AATCCTTCATACCTTGCTCAAAAGGAGACTCTGAGTCAGTAGCA
1 AATCCTTCATACCTTGCTCAAAAGGAGACTCTGAGTCAGTAGCA
*
28205176 AATCCTTCATACCTTGCTCAAAAGGAGACTCTGAGTTAGTAGCA
1 AATCCTTCATACCTTGCTCAAAAGGAGACTCTGAGTCAGTAGCA
28205220 GTGTCGCTCA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (44 bp):
AATCCTTCATACCTTGCTCAAAAGGAGACTCTGAGTCAGTAGCA
Found at i:28206461 original size:24 final size:26
Alignment explanation
Indices: 28206410--28206478 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
28206400 ACATATATTC
**
28206410 TCAATTCAATCACAATTTCTCACACTT
1 TCAATTCAATCA-TTTTTCTCACACTT
28206437 TCAATTCAATCATTTTTC-CAC-CTT
1 TCAATTCAATCATTTTTCTCACACTT
*
28206461 TCAA-TCAATAATTATTTC
1 TCAATTCAATCATT-TTTC
28206479 ACAAATTCAC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
23 8 0.21
24 11 0.29
25 3 0.08
26 4 0.11
27 12 0.32
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (26 bp):
TCAATTCAATCATTTTTCTCACACTT
Found at i:28206630 original size:3 final size:3
Alignment explanation
Indices: 28206622--28206660 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
28206612 ATTCCCACTC
* * *
28206622 ATA ATA ATA ATA ATA ACA ATA CTA ATA ATA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28206661 CTTACCTCAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:28207467 original size:19 final size:19
Alignment explanation
Indices: 28207422--28207461 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
28207412 TTTGTTTTGT
*
28207422 TTTTATTT-CTTTACTTTC
1 TTTTATTTACTTTACTTTA
28207440 TTTTATTTACTTTACTTTA
1 TTTTATTTACTTTACTTTA
28207459 TTT
1 TTT
28207462 CTTTTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTATTTACTTTACTTTA
Found at i:28211713 original size:19 final size:19
Alignment explanation
Indices: 28211697--28211741 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
28211687 TTATGAAACT
*
28211697 TAATGCATATGATGAAATG
1 TAATGCAGATGATGAAATG
*
28211716 TAATGCAGATGAATAAAATG
1 TAATGCAGATG-ATGAAATG
28211736 -AATGCA
1 TAATGCA
28211742 AAAAGAGGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.27
Consensus pattern (19 bp):
TAATGCAGATGATGAAATG
Found at i:28215295 original size:3 final size:3
Alignment explanation
Indices: 28215287--28215363 Score: 57
Period size: 3 Copynumber: 25.3 Consensus size: 3
28215277 ATGCATAAAC
* * * * *
28215287 AAT AAT AAT AAT GAT GAA- AAT GAT AAC AAT AAT AAT GAT AAT AAC
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
28215332 AAT AAC ATT AAT AAT ATT AAT AAT GAAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT A
28215364 TAAATGTTTG
Statistics
Matches: 55, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
2 2 0.04
3 49 0.89
4 4 0.07
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:28215336 original size:24 final size:24
Alignment explanation
Indices: 28215290--28215354 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
28215280 CATAAACAAT
**
28215290 AATAATAATGATGAA-AATGATAAC
1 AATAATAATGAT-AATAACAATAAC
28215314 AATAATAATGATAATAACAATAAC
1 AATAATAATGATAATAACAATAAC
*
28215338 ATTAATAAT-ATTAATAA
1 AATAATAATGA-TAATAA
28215355 TGAATAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 3 0.08
24 33 0.92
ACGTcount: A:0.60, C:0.05, G:0.06, T:0.29
Consensus pattern (24 bp):
AATAATAATGATAATAACAATAAC
Found at i:28222534 original size:16 final size:17
Alignment explanation
Indices: 28222502--28222534 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
28222492 TGTAGTCCAC
*
28222502 ATGTTCAATCTATTTGA
1 ATGTTCAATCGATTTGA
28222519 ATGTTC-ATCGATTTGA
1 ATGTTCAATCGATTTGA
28222535 TTTTTATCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.45
Consensus pattern (17 bp):
ATGTTCAATCGATTTGA
Found at i:28223618 original size:23 final size:21
Alignment explanation
Indices: 28223587--28223643 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 21
28223577 ATTTTTAAAA
*
28223587 TTTAAAATTTGTTTTATATATTT
1 TTTAAAATTT-TTTT-TAAATTT
*
28223610 TTTAGAATTTTTTTTAAATTT
1 TTTAAAATTTTTTTTAAATTT
28223631 TTATAAATATTTT
1 TT-TAAA-ATTTT
28223644 GAATTTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 8 0.28
22 7 0.24
23 14 0.48
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.65
Consensus pattern (21 bp):
TTTAAAATTTTTTTTAAATTT
Found at i:28223675 original size:20 final size:18
Alignment explanation
Indices: 28223621--28223685 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 18
28223611 TTAGAATTTT
*
28223621 TTTTAAATTTTTATAAATA
1 TTTTGAATTTTTA-AAATA
*
28223640 TTTTGAATTTTAAAAACTA
1 TTTTGAATTTTTAAAA-TA
28223659 TTTTGAATTTTTGAAAATTA
1 TTTTGAATTTTT-AAAA-TA
28223679 TTTTGAA
1 TTTTGAA
28223686 ACTTTTTTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
18 3 0.08
19 24 0.60
20 13 0.32
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (18 bp):
TTTTGAATTTTTAAAATA
Found at i:28224609 original size:26 final size:27
Alignment explanation
Indices: 28224571--28224621 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
28224561 ACCAAAGTCT
28224571 ATAACAGATACAGATAT-CAGAATCAG
1 ATAACAGATACAGATATACAGAATCAG
28224597 ATAACCAGA-ACAGATATACAGAATC
1 ATAA-CAGATACAGATATACAGAATC
28224622 CTACCCCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.51, C:0.18, G:0.14, T:0.18
Consensus pattern (27 bp):
ATAACAGATACAGATATACAGAATCAG
Found at i:28227802 original size:51 final size:51
Alignment explanation
Indices: 28227737--28227850 Score: 158
Period size: 51 Copynumber: 2.2 Consensus size: 51
28227727 AGAAAGGATG
* *
28227737 AAAATGGAGAAATGGAGAAATGGAAAACATTTG-GAATGATTATGGTTTTCTCC
1 AAAAT-GA-AAATGGAGAAAT-GAAAACATTTGAAAATGAATATGGTTTTCTCC
* *
28227790 AAAATGAAAATGGAGAAATGAAATCATTTGAAAATGAATGTGGTTTTCTCC
1 AAAATGAAAATGGAGAAATGAAAACATTTGAAAATGAATATGGTTTTCTCC
28227841 AAAATGAAAA
1 AAAATGAAAA
28227851 ATAAAAATGA
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
50 10 0.18
51 39 0.70
52 2 0.04
53 5 0.09
ACGTcount: A:0.45, C:0.07, G:0.21, T:0.27
Consensus pattern (51 bp):
AAAATGAAAATGGAGAAATGAAAACATTTGAAAATGAATATGGTTTTCTCC
Found at i:28231209 original size:5 final size:5
Alignment explanation
Indices: 28231201--28231285 Score: 138
Period size: 5 Copynumber: 17.0 Consensus size: 5
28231191 TTTATTTAAT
28231201 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
28231251 ATATA ATATA ATATA TTATATA ATA-A A-ATA ATATA
1 ATATA ATATA ATATA --ATATA ATATA ATATA ATATA
28231286 CATAACATAA
Statistics
Matches: 76, Mismatches: 0, Indels: 8
0.90 0.00 0.10
Matches are distributed among these distances:
3 1 0.01
4 4 0.05
5 66 0.87
7 5 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:28232627 original size:22 final size:23
Alignment explanation
Indices: 28232597--28232640 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
28232587 TTTGAGGTTA
28232597 AAAAAATAAGA-AAAAA-AAGTTT
1 AAAAAATAA-ATAAAAAGAAGTTT
*
28232619 AAAATATAAATAAAAAGAAGTT
1 AAAAAATAAATAAAAAGAAGTT
28232641 AGAAAGGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 1 0.05
22 13 0.68
23 5 0.26
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.20
Consensus pattern (23 bp):
AAAAAATAAATAAAAAGAAGTTT
Found at i:28233734 original size:25 final size:25
Alignment explanation
Indices: 28233674--28233736 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 25
28233664 ATCGGATTGG
*
28233674 TTAT-TGTAAAGGAAATGTTATGGT
1 TTATATGTAAAGGAAATGTTACGGT
28233698 TATATATGTAAAGGAAATGTTACGGT
1 T-TATATGTAAAGGAAATGTTACGGT
28233724 TTATATGTAAAGG
1 TTATATGTAAAGG
28233737 TACACTATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
24 1 0.03
25 15 0.42
26 20 0.56
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.38
Consensus pattern (25 bp):
TTATATGTAAAGGAAATGTTACGGT
Found at i:28237103 original size:12 final size:12
Alignment explanation
Indices: 28237086--28237116 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
28237076 TCTAAACAAT
28237086 ATAATAATCCTA
1 ATAATAATCCTA
28237098 ATAATAATCCTA
1 ATAATAATCCTA
*
28237110 AAAATAA
1 ATAATAA
28237117 AATTCAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (12 bp):
ATAATAATCCTA
Found at i:28239353 original size:20 final size:20
Alignment explanation
Indices: 28239314--28239353 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
28239304 GTAAGAAAAT
* *
28239314 GAAAATAAATAAAATTATCA
1 GAAAACAAATAAAATCATCA
*
28239334 GAAAACAAATAATATCATCA
1 GAAAACAAATAAAATCATCA
28239354 TAAATATAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.23
Consensus pattern (20 bp):
GAAAACAAATAAAATCATCA
Found at i:28239932 original size:4 final size:4
Alignment explanation
Indices: 28239923--28239948 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
28239913 ATCATCACAT
28239923 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
28239949 GTCTGTGTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:28246891 original size:2 final size:2
Alignment explanation
Indices: 28246886--28246929 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
28246876 TTTACTTAAG
28246886 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28246925 T- TA TA
1 TA TA TA
28246930 ATAAAAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 4 0.11
2 34 0.89
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:28246948 original size:10 final size:10
Alignment explanation
Indices: 28246887--28246955 Score: 50
Period size: 10 Copynumber: 6.7 Consensus size: 10
28246877 TTACTTAAGT
28246887 ATATATATATA
1 ATATATA-ATA
28246898 TATATATATATA
1 -ATATATA-ATA
* *
28246910 TTATATTATA
1 ATATATAATA
* *
28246920 TTATATTATA
1 ATATATAATA
*
28246930 ATA-AAAATA
1 ATATATAATA
28246939 ATATATAATA
1 ATATATAATA
*
28246949 ATGTATA
1 ATATATA
28246956 TTATAAATAA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
9 7 0.14
10 26 0.53
11 5 0.10
12 11 0.22
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (10 bp):
ATATATAATA
Found at i:28246991 original size:5 final size:5
Alignment explanation
Indices: 28246964--28247025 Score: 51
Period size: 5 Copynumber: 12.6 Consensus size: 5
28246954 TATTATAAAT
*
28246964 AAAAG -AAAG AAACG AAACA- AAAAG AAAA- AGAAAG -AAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAA-AG AAAAG AAAAG A-AAAG AAAAG AAAAG AAAAG
*
28247012 AAAAAG GAAAG AAA
1 -AAAAG AAAAG AAA
28247026 GGAAGGAGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
4 10 0.22
5 31 0.67
6 5 0.11
ACGTcount: A:0.77, C:0.03, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:28246997 original size:25 final size:24
Alignment explanation
Indices: 28246964--28247026 Score: 92
Period size: 25 Copynumber: 2.5 Consensus size: 24
28246954 TATTATAAAT
28246964 AAAAGAAAGAAACGAAACA-AAAAGA
1 AAAAGAAAGAAA-GAAA-AGAAAAGA
28246989 AAAAGAAAGAAAGAAAAGAAAAGA
1 AAAAGAAAGAAAGAAAAGAAAAGA
28247013 AAAAGGAAAGAAAG
1 AAAA-GAAAGAAAG
28247027 GAAGGAGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
23 1 0.03
24 14 0.39
25 21 0.58
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (24 bp):
AAAAGAAAGAAAGAAAAGAAAAGA
Found at i:28247009 original size:29 final size:29
Alignment explanation
Indices: 28246965--28247026 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
28246955 ATTATAAATA
*
28246965 AAAGAAAGAAACG-AAACAAAAAGAAAAAG
1 AAAGAAAGAAAAGAAAACAAAAAG-AAAAG
* *
28246994 AAAGAAAGAAAAGAAAAGAAAAAGGAAAG
1 AAAGAAAGAAAAGAAAACAAAAAGAAAAG
28247023 AAAG
1 AAAG
28247027 GAAGGAGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (29 bp):
AAAGAAAGAAAAGAAAACAAAAAGAAAAG
Found at i:28247929 original size:41 final size:38
Alignment explanation
Indices: 28247883--28247991 Score: 121
Period size: 41 Copynumber: 2.8 Consensus size: 38
28247873 GACTTCGAGT
*
28247883 TGATGAGACACTAGGTGTCAATTTACTACTTTGGATTAAT
1 TGATGAGACACTAGGTGTCAATTT--TACTTTGGATTAAC
* * *
28247923 TCGATGAGGCACTAGGTGCCAA-TTTACTTTGGTTTAAC
1 T-GATGAGACACTAGGTGTCAATTTTACTTTGGATTAAC
*
28247961 TGATGAGACACTGGGTGTCTAATTATTACTT
1 TGATGAGACACTAGGTGTC-AATT-TTACTT
28247992 CGAATTATCC
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
37 15 0.26
38 15 0.26
39 1 0.02
40 9 0.16
41 18 0.31
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.37
Consensus pattern (38 bp):
TGATGAGACACTAGGTGTCAATTTTACTTTGGATTAAC
Found at i:28249969 original size:18 final size:18
Alignment explanation
Indices: 28249946--28249981 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
28249936 ATAATATTTT
28249946 TCAT-AAAAATATTAAAAA
1 TCATAAAAAAT-TTAAAAA
28249964 TCATAAAAAATTTAAAAA
1 TCATAAAAAATTTAAAAA
28249982 ATAAGCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (18 bp):
TCATAAAAAATTTAAAAA
Found at i:28249972 original size:10 final size:9
Alignment explanation
Indices: 28249950--28250259 Score: 51
Period size: 10 Copynumber: 32.4 Consensus size: 9
28249940 TATTTTTCAT
*
28249950 AAAAATATT
1 AAAAATATA
28249959 AAAAATCATA
1 AAAAAT-ATA
*
28249969 AAAAATTTA
1 AAAAATATA
*
28249978 AAAAATAAGCA
1 AAAAAT-A-TA
*
28249989 AAAAACCA-A
1 AAAAA-TATA
* *
28249998 GAAAAATTTC
1 -AAAAATATA
*
28250008 TAAAATATA
1 AAAAATATA
** *
28250017 TTAAATATT
1 AAAAATATA
28250026 AAAAATACT-
1 AAAAATA-TA
*
28250035 AAAATTGATA
1 AAAAAT-ATA
* *
28250045 TAAACTTATA
1 AAAAAT-ATA
*
28250055 AAAATTATGA
1 AAAAATAT-A
*
28250065 AAGAATA-A
1 AAAAATATA
* *
28250073 AATATTATA
1 AAAAATATA
28250082 -AAAATAT-
1 AAAAATATA
28250089 AAAAATAT-
1 AAAAATATA
28250097 AAAAATATA
1 AAAAATATA
*
28250106 AAAAATTCTA
1 AAAAA-TATA
*
28250116 ATAAAT-TA
1 AAAAATATA
*
28250124 TAAAATCAATA
1 AAAAAT--ATA
* *
28250135 AAACATATT
1 AAAAATATA
*
28250144 TAAAATACTTA
1 AAAAATA--TA
* *
28250155 AAATGTTATAAA
1 AAA---AATATA
28250167 AAAAAGTATA
1 AAAAA-TATA
28250177 AAAAATCATAA
1 AAAAAT-AT-A
28250188 AAAAATTATA
1 AAAAA-TATA
* *
28250198 AAAAATTGTT
1 AAAAA-TATA
*
28250208 AAAAATATT
1 AAAAATATA
*
28250217 AAAATTGAT-
1 AAAAAT-ATA
* *
28250226 ATAAATTTA
1 AAAAATATA
28250235 TAAAAATATTA
1 -AAAAATA-TA
28250246 AAAAATCATA
1 AAAAAT-ATA
28250256 AAAA
1 AAAA
28250260 CTTGAACTAG
Statistics
Matches: 219, Mismatches: 51, Indels: 61
0.66 0.15 0.18
Matches are distributed among these distances:
8 33 0.15
9 69 0.32
10 82 0.37
11 27 0.12
12 5 0.02
14 3 0.01
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (9 bp):
AAAAATATA
Found at i:28250090 original size:18 final size:18
Alignment explanation
Indices: 28250008--28250129 Score: 78
Period size: 17 Copynumber: 6.8 Consensus size: 18
28249998 GAAAAATTTC
*
28250008 TAAAATATATTAAATA-T-
1 TAAAA-ATATAAAATATTA
28250025 TAAAAATACTAAAAT-TGATA
1 TAAAAATA-TAAAATAT--TA
**
28250045 TAAACTTATAAAA-ATTA
1 TAAAAATATAAAATATTA
*
28250062 TGAAAGA-ATAAAATATTA
1 T-AAAAATATAAAATATTA
28250080 TAAAAATATAAAA-A-TA
1 TAAAAATATAAAATATTA
* *
28250096 TAAAAATATAAAAAATTC
1 TAAAAATATAAAATATTA
28250114 TAATAAATTATAAAAT
1 TAA-AAA-TATAAAAT
28250130 CAATAAAACA
Statistics
Matches: 84, Mismatches: 8, Indels: 23
0.73 0.07 0.20
Matches are distributed among these distances:
16 18 0.21
17 25 0.30
18 18 0.21
19 10 0.12
20 13 0.15
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (18 bp):
TAAAAATATAAAATATTA
Found at i:28250091 original size:8 final size:8
Alignment explanation
Indices: 28250009--28250109 Score: 69
Period size: 8 Copynumber: 11.5 Consensus size: 8
28249999 AAAAATTTCT
28250009 AAAATATA
1 AAAATATA
*
28250017 TTAAATATTA
1 -AAAATA-TA
28250027 AAAATACTA
1 AAAATA-TA
28250036 AAATTGATATA
1 AAA---ATATA
**
28250047 AACTTATA
1 AAAATATA
28250055 AAAATTATGA
1 AAAA-TAT-A
28250065 AAGAATA-A
1 AA-AATATA
*
28250073 AATATTATA
1 AA-AATATA
28250082 AAAATATA
1 AAAATATA
28250090 AAAATATA
1 AAAATATA
28250098 AAAATATA
1 AAAATATA
28250106 AAAA
1 AAAA
28250110 ATTCTAATAA
Statistics
Matches: 74, Mismatches: 10, Indels: 17
0.73 0.10 0.17
Matches are distributed among these distances:
8 37 0.50
9 21 0.28
10 7 0.09
11 6 0.08
12 3 0.04
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (8 bp):
AAAATATA
Found at i:28250211 original size:20 final size:20
Alignment explanation
Indices: 28250188--28250264 Score: 63
Period size: 19 Copynumber: 4.0 Consensus size: 20
28250178 AAAATCATAA
*
28250188 AAAAATTATAAAAAATTGTT
1 AAAAATTATAAAAAATTGAT
*
28250208 AAAAA-TAT-TAAAATTGAT
1 AAAAATTATAAAAAATTGAT
*
28250226 ATAAATTTATAAAAATATT-A-
1 A-AAAATTATAAAAA-ATTGAT
* *
28250246 AAAAATCATAAAAACTTGA
1 AAAAATTATAAAAAATTGA
28250265 ACTAGGTTGG
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
18 11 0.24
19 18 0.40
20 9 0.20
21 4 0.09
22 3 0.07
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.32
Consensus pattern (20 bp):
AAAAATTATAAAAAATTGAT
Found at i:28250903 original size:21 final size:20
Alignment explanation
Indices: 28250866--28250905 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
28250856 ATTGTTTTTA
**
28250866 TAATTTTTTTTTCTAATTTC
1 TAATTTTTTTTAATAATTTC
28250886 TAATTTATTTTTAATAATTT
1 TAATTT-TTTTTAATAATTT
28250906 TATGCAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (20 bp):
TAATTTTTTTTAATAATTTC
Found at i:28251483 original size:18 final size:18
Alignment explanation
Indices: 28251448--28251481 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
28251438 GTTCACTCTG
28251448 TTTTTCAGTTTTACTTTA
1 TTTTTCAGTTTTACTTTA
*
28251466 TTTTT-AGTTTTGCTTT
1 TTTTTCAGTTTTACTTT
28251482 TAAAAATGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.12, C:0.09, G:0.09, T:0.71
Consensus pattern (18 bp):
TTTTTCAGTTTTACTTTA
Found at i:28254343 original size:50 final size:50
Alignment explanation
Indices: 28254225--28254410 Score: 266
Period size: 50 Copynumber: 3.7 Consensus size: 50
28254215 TAAATGATGG
* * * * * * * *
28254225 TCACATGTGTAGTACTAAGTGAAGGCTACAATGTGTATCG-AGAAGCTTTGG
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTA-AAAC-TTGA
28254276 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGA
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGA
28254326 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGA
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGA
*
28254376 TCATGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTG
28254411 TATCGAATGA
Statistics
Matches: 125, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
50 87 0.70
51 37 0.30
52 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGA
Found at i:28255551 original size:24 final size:24
Alignment explanation
Indices: 28255524--28255575 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
28255514 TTAGTAAGTC
*
28255524 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
28255548 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
28255572 AAAT
1 AAAT
28255576 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:28257304 original size:44 final size:44
Alignment explanation
Indices: 28257234--28257324 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 44
28257224 AATTCTATTT
28257234 TTAGTTTCCCACTTAAACATTAATTAGTGTAGGTTATTTTAATA
1 TTAGTTTCCCACTTAAACATTAATTAGTGTAGGTTATTTTAATA
* * * *
28257278 TTAGTTTCTCACTTAAGC-TCTGATTAGTGTTGGTTATTTTAATA
1 TTAGTTTCCCACTTAAACAT-TAATTAGTGTAGGTTATTTTAATA
28257322 TTA
1 TTA
28257325 TTAGACCTAC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 1 0.02
44 41 0.98
ACGTcount: A:0.27, C:0.11, G:0.13, T:0.48
Consensus pattern (44 bp):
TTAGTTTCCCACTTAAACATTAATTAGTGTAGGTTATTTTAATA
Found at i:28262893 original size:45 final size:45
Alignment explanation
Indices: 28262841--28263063 Score: 251
Period size: 45 Copynumber: 5.0 Consensus size: 45
28262831 GGATTAGACT
* *
28262841 GGATATCCATATAAATAAAGGTTGTTGCTAAGTGCTGATTCCACC
1 GGATATCCATGTAAATAAAGGTGGTTGCTAAGTGCTGATTCCACC
* *
28262886 GGATATCCATGTAAGT--AGGTGGTTGCTAACTGCTGATTCCACC
1 GGATATCCATGTAAATAAAGGTGGTTGCTAAGTGCTGATTCCACC
* * * * *
28262929 AGATATTC-TCG-AATCTAAAGATGGTTGCTAAGTGCTAATTCCACC
1 GGATATCCAT-GTAA-ATAAAGGTGGTTGCTAAGTGCTGATTCCACC
* *
28262974 GGATATCCATGTAAGT-AAGGTGGTTGCTAAGTGCCGATTCCACC
1 GGATATCCATGTAAATAAAGGTGGTTGCTAAGTGCTGATTCCACC
* * *
28263018 GGATAACCTTG-AATATAAAGGTGGTTGCTAAATGCTGATTCCACC
1 GGATATCCATGTAA-ATAAAGGTGGTTGCTAAGTGCTGATTCCACC
28263063 G
1 G
28263064 TGTAATTATT
Statistics
Matches: 149, Mismatches: 21, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
42 3 0.02
43 35 0.23
44 35 0.23
45 73 0.49
46 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (45 bp):
GGATATCCATGTAAATAAAGGTGGTTGCTAAGTGCTGATTCCACC
Found at i:28263059 original size:89 final size:88
Alignment explanation
Indices: 28262855--28263063 Score: 310
Period size: 89 Copynumber: 2.4 Consensus size: 88
28262845 ATCCATATAA
* *
28262855 ATAAAGGTTGTTGCTAAGTGCTGATTCCACCGGATATCCATGTAAGTAGGTGGTTGCTAACTGCT
1 ATAAAGGTGGTTGCTAAGTGCTGATTCCACCGGATATCCATGTAAGTAGGTGGTTGCTAACTGCC
**
28262920 GATTCCACCAGATATTCTCGAAT
66 GATTCCACCAGATAACCTCGAAT
* * * *
28262943 CTAAAGATGGTTGCTAAGTGCTAATTCCACCGGATATCCATGTAAGTAAGGTGGTTGCTAAGTGC
1 ATAAAGGTGGTTGCTAAGTGCTGATTCCACCGGATATCCATGTAAGT-AGGTGGTTGCTAACTGC
* *
28263008 CGATTCCACCGGATAACCTTGAAT
65 CGATTCCACCAGATAACCTCGAAT
*
28263032 ATAAAGGTGGTTGCTAAATGCTGATTCCACCG
1 ATAAAGGTGGTTGCTAAGTGCTGATTCCACCG
28263064 TGTAATTATT
Statistics
Matches: 106, Mismatches: 14, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
88 43 0.41
89 63 0.59
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (88 bp):
ATAAAGGTGGTTGCTAAGTGCTGATTCCACCGGATATCCATGTAAGTAGGTGGTTGCTAACTGCC
GATTCCACCAGATAACCTCGAAT
Found at i:28265374 original size:32 final size:32
Alignment explanation
Indices: 28265337--28265401 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
28265327 CCGATTTAAG
28265337 TGGATCCCTCCCCTTTTATTAAAATTAAAATA
1 TGGATCCCTCCCCTTTTATTAAAATTAAAATA
28265369 TGGATCCCTCCCCTTTTATTAAAATTAAAATA
1 TGGATCCCTCCCCTTTTATTAAAATTAAAATA
28265401 T
1 T
28265402 ACTTTTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.38
Consensus pattern (32 bp):
TGGATCCCTCCCCTTTTATTAAAATTAAAATA
Found at i:28265838 original size:30 final size:31
Alignment explanation
Indices: 28265804--28265863 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
28265794 AAACCTTTTA
*
28265804 TTTTCCCCCAAAATTTTTACTTCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTTCCTTCCCAC
* *
28265834 TTTTCCCCTAAAACTTTTATTTCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTTCCTTCCCA
28265864 TCCCACCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.37, G:0.00, T:0.43
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTTCCTTCCCAC
Found at i:28284245 original size:43 final size:43
Alignment explanation
Indices: 28284198--28284323 Score: 101
Period size: 43 Copynumber: 3.1 Consensus size: 43
28284188 TATTTTATTA
28284198 TTTATCATCTTTTTATCTTTTACTTTCCAATTTAGTCATTTTC
1 TTTATCATCTTTTTATCTTTTACTTTCCAATTTAGTCATTTTC
* ** * * * *
28284241 TTTAT--T-TAGTTT-TCTATGGA---T-GAA-TCA-TCATATTA
1 TTTATCATCT-TTTTATCT-TTTACTTTCCAATTTAGTCATTTTC
28284276 TTTATCATCTTTTTATCTTTTACTTTCCAATTTAGTCATTTTC
1 TTTATCATCTTTTTATCTTTTACTTTCCAATTTAGTCATTTTC
28284319 TTTAT
1 TTTAT
28284324 TTAGTTTTCT
Statistics
Matches: 57, Mismatches: 14, Indels: 24
0.60 0.15 0.25
Matches are distributed among these distances:
35 11 0.19
36 2 0.04
37 8 0.14
38 5 0.09
40 5 0.09
41 8 0.14
42 2 0.04
43 16 0.28
ACGTcount: A:0.21, C:0.15, G:0.05, T:0.59
Consensus pattern (43 bp):
TTTATCATCTTTTTATCTTTTACTTTCCAATTTAGTCATTTTC
Done.